EP1002134B1 - Detection of wheat fungal pathogens using the polymerase chain reaction - Google Patents

Detection of wheat fungal pathogens using the polymerase chain reaction Download PDF

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EP1002134B1
EP1002134B1 EP98945123A EP98945123A EP1002134B1 EP 1002134 B1 EP1002134 B1 EP 1002134B1 EP 98945123 A EP98945123 A EP 98945123A EP 98945123 A EP98945123 A EP 98945123A EP 1002134 B1 EP1002134 B1 EP 1002134B1
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seq
pair
primers
fusarium
primer
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EP1002134A1 (en
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James Joseph Beck
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Syngenta Participations AG
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/37—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from fungi

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  • the present invention relates to the use of species-specific primers in polymerase chain reaction assays for the detection of fungal pathogens of wheat.
  • the use of these primers enables the detection of specific isolates of fungal pathogens and the monitoring of disease development in plant populations.
  • the present invention is drawn to methods of identification of different pathotypes of plant pathogenic fungi.
  • the invention provides Internal Transcribed Spacer (ITS) DNA sequences that show variability between different fungal pathotypes.
  • ITS Internal Transcribed Spacer
  • DNA sequences are useful in the method of the invention as they can be used to derive primers for use in polymerase chain reaction (PCR)-based diagnostic assays. These primers generate unique fragments in PCR reactions in which the DNA template is provided by specific fungal pathotypes and can thus be used to identify the presence or absence of specific pathotypes in host plant material before the onset of disease symptoms.
  • the invention provides ITS1 and ITS2 DNA sequences for the pathogens Fusarium poae, Fusarium avenaceum, and Microdochium nivale. In another preferred embodiment, the invention provides ITS-derived diagnostic primers for the detection of Fusarium spp. and Microdochium nivale.
  • This invention provides the possibility of assessing potential damage in a specific crop variety-pathogen strain relationship and of utilizing judiciously the diverse armory of fungicides that is available. Furthermore, the invention can be used to provide detailed information on the development and spread of specific pathogen races over extended geographical areas. The invention provides a method of detection that is especially suitable for diseases with a long latent phase. Kits useful in the practice of the invention are also provided. The kits find particular use in the identification of the fungal pathogens Fusarium spp. and Microdochium nivale.
  • the present invention provides unique DNA sequences that are useful in identifying different pathotypes of plant pathogenic fungi.
  • the DNA sequences can be used as primers in PCR-based analysis for the identification of fungal pathotypes.
  • the DNA sequences of the invention include the Internal Transcribed Spacer (ITS) sequences of the ribosomal RNA gene regions of particular fungal pathogens as well as primers derived from these regions that are capable of identifying the particular pathogen. These ITS DNA sequences from different pathotypes within a pathogen species or genus, which vary between the different members of the species or genus, can be used to identify those specific members.
  • ITS Internal Transcribed Spacer
  • 5,585,238 describes primers derived from the ITS sequences of the ribosomal RNA gene region of strains of Septoria, Pseudocercosporella, and Mycosphaerella and their use in the identification of these fungal isolates using PCR-based techniques.
  • WO 95/29260 describes primers derived from the ITS sequences of the ribosomal RNA gene region of strains of Fusarium and their use in the identification of these fungal isolates using PCR-based techniques.
  • EP 08590101 describes primers derived from the ITS sequences of the ribosomal RNA gene region of strains of Cercospora, Helminthosporium, Kabatiella, and Puccinia and their use in the identification of these fungal isolates using PCR-based techniques.
  • Ribosomal genes are suitable for use as molecular probe targets because of their high copy number.
  • the non-transcribed and transcribed spacer sequences are usually poorly conserved and are thus suitable as target sequences for the detection of recent evolutionary divergence.
  • Fungal rRNA genes are organized in units, each of which encodes three mature subunits of 18S (small subunit), 5.8S, and 28S (large subunit). These subunits are separated by two Internal Transcribed Spacers, ITS1 and ITS2, of around 300 bp (White et al., 1990; In: PCR Protocols; Eds.: Innes et al.; pages 315-322).
  • the transcriptional units are separated by non-transcribed spacer sequences (NTSs).
  • the ITS and NTS sequences are particularly suitable for the detection of specific pathotypes of different fungal pathogens.
  • the DNA sequences of the invention are from the Internal Transcribed Spacer sequences of the ribosomal RNA gene region of different plant pathogens.
  • the ITS DNA sequences from different pathotypes within a pathogen species or genus vary among the different members of the species or genus. Once having determined the ITS sequences of a pathogen, these sequences can be aligned with other ITS sequences. In this manner, primers can be derived from the ITS sequences. That is, primers can be designed based on regions within the ITS sequences that contain the greatest differences in sequence among the fungal pathotypes. These sequences and primers based on these sequences can be used to identify specific pathogens.
  • ITS DNA sequences from Fusarium poae, Microdochium nivale, and Fusarium avenaceum are disclosed in SEQ ID NOs: 22-24, respectively.
  • Sequences of representative oligonucleotide primers derived from these ITS sequences are disclosed in SEQ ID NOs: 7-18. The sequences find use in the PCR-based identification of the pathotypes of interest.
  • isolated DNA molecules comprising an Internal Transcribed Spacer sequence selected from ITS1 of Fusarium poae, ITS2 of Fusarium poae, ITS1 of Microdochium nivale, ITS2 of Microdochium nivale, ITS1 of Fusarium avenaceum, and ITS2 of Fusarium avenaceum.
  • ITS1 of Fusarium poae comprises nucleotides 31-180 of SEQ ID NO:22, wherein ITS2 of Fusarium poae comprises nucleotides 338-489 of SEQ ID NO:22, wherein ITS1 of Microdochium nivale comprises nucleotides 31-175 of SEQ ID NO:23, wherein ITS2 of Microdochium nivale comprises nucleotides 333-499 of SEQ ID NO:23, wherein ITS1 of Fusarium avenaceum comprises nucleotides 31-181 of SEQ ID NO:24, and wherein ITS2 of Fusarium avenaceum comprises nucleotides 339-504 of SEQ ID NO:24.
  • the ITS DNA sequences of the invention can be cloned from fungal pathogens by methods known in the art. In general, the methods for the isolation of DNA from fungal isolates are known. See, Raeder & Broda (1985) Letters in Applied Microbiology 2 :17-20; Lee et al. (1990) Fungal Genetics Newsletter 35 :23-24; and Lee and Taylor (1990) In: PCR Protocols: A Guide to Methods and Applications, Innes et al. (Eds.); pages 282-287.
  • the ITS sequences of interest can be determined by PCR amplification.
  • primers to amplify the entire ITS region were designed according to White et al. (1990; In: PCR Protocols; Eds.: Innes et al. pages 315-322), and the amplified ITS sequence was subcloned into the pCRII cloning vector.
  • the subcloned sequence included the left hand ITS (ITS1), the right hand ITS (ITS2), as well as the centrally located 5.8S rRNA gene. This was undertaken for several species of Fusarium, including Fusarium poae and Fusarium avenaceum, as well as Microdochium nivale.
  • the determined ITS sequences were compared within each pathogen group to locate divergences that might be useful to test in PCR to distinguish the different species and/or strains.
  • the ITS DNA sequences that were determined are shown in SEQ ID NOs: 19-24 and the comparative alignment is shown in FIGURE 1. From the identification of divergences, numerous primers were synthesized and tested in PCR-amplification. Templates used for PCR-amplification testing were firstly purified pathogen DNA, and subsequently DNA isolated from infected host plant tissue. Thus, it was possible to identify pairs of primers that were diagnostic, i.e. that identified one particular pathogen species or strain but not another species or strain of the same pathogen.
  • Primers were also designed to regions highly conserved among the species to develop genus-specific primers as well as primers that will identify any of several fungal pathogens that cause a particular disease. For example, primers were developed to detect Fusarium caused by various fungal pathogens, including Fusarium spp. and Microdochium nivale.
  • Preferred primer combinations are able to distinguish between the different species or strains in infected host tissue, i.e. host tissue that has previously been infected with a specific pathogen species or strain.
  • This invention provides numerous primer combinations that fulfill this criterion for different Fusarium spp. and Microdochium nivale.
  • the primers of the invention are designed based on sequence differences among the fungal ITS regions. A minimum of one base pair difference between sequences can permit design of a discriminatory primer. Primers designed to a specific fungal DNA's ITS region can be used in combination with a primer made to a conserved sequence region within the ribosomal DNA's coding region to amplify species-specific PCR fragments.
  • primers should have a theoretical melting temperature between about 60 to about 70 degree °C to achieve good sensitivity and should be void of significant secondary structure and 3' overlaps between primer combinations.
  • Primers generally have sequence identity with at least about 5-10 contiguous nucleotide bases of ITS1 or ITS2, preferably with at least 10 contiguous nucleotide bases of ITS1 or ITS2. In preferred embodiments, primers are anywhere from approximately 5-30 nucleotide bases long.
  • oligonucleotide primer for use in identification of a fungal pathogen, wherein said oligonucleotide primer is selected from the group consisting of SEQ ID NO's:7-15.
  • a further embodiment of the present invention is a pair of oligonucleotide primers for use in the amplification-based detection of a fungal Internal Transcribed Spacer DNA sequence, wherein at least one of said primers is the oligonucleotide primer according to the invention.
  • Preferred is a pair of oligonucleotide primers, wherein said pair is selected from the oligonucleotide primers according to claim 8 to 12.
  • the present invention relates to method for the detection of a fungal pathogen, comprising the steps of:
  • kits containing the elements necessary to carry out the process.
  • a kit may comprise a carrier being compartmentalized to receive in close confinement therein one or more container, such as tubes or vials.
  • One of the containers may contain unlabeled or detectably labeled DNA primers.
  • the labeled DNA primers may be present in lyophilized form or in an appropriate buffer as necessary.
  • One or more containers may contain one or more enzymes or reagents to be utilized in PCR reactions. These enzymes may be present by themselves or in admixtures, in lyophilized form or in appropriate buffers.
  • kit may contain all of the additional elements necessary to carry out the technique of the invention, such as buffers, extraction reagents, enzymes, pipettes, plates, nucleic acids, nucleoside triphosphates, filter paper, gel materials, transfer materials, autoradiography supplies, and the like.
  • a diagnostic kit used in detecting a fungal pathogen comprising the pair of primers for use in the amplification-based detection of a fungal Internal Transcribed Spacer DNA sequence, wherein at least one of said primers is the oligonucleotide primer according to the invention.
  • Fungi are grown in 150 ml potato dextrose broth inoculated with mycelial fragments from PDA (Potato Dextrose Agar) cultures. Cultures are incubated on an orbital shaker at 28°C for 7-11 days. Mycelia are pelleted by centrifugation and then ground in liquid nitrogen, and total genomic DNA is extracted using the protocol of Lee and Taylor (1990; In: PCR Protocols: A Guide to Methods and Applications Eds.: Innes et al.; pages 282-287).
  • Table 1 Source of Test Isolates Isolate Organism Origin Source 69 Microdochium nivale Novartis-Basel 1 72 Microdochium nivale Novartis-Basel 1 92 Microdochium nivale var. majus Novartis-Basel 1 93 Microdochium nivale var. majus Novartis-Basel 1 520 Microdochium nivale Novartis-Basel 1 18222 Microdochium nivale Scotland ATCC 2 T-0427 Fusarium poae Lancaster County, PA USA P. Nelson 3 T-0534 Fusarium poae Rock Springs. PA USA P. Nelson 3 T-0756 Fusarium poae Unionville. PA USA P.
  • Approximately 550-bp long internal transcribed spacer region fragments are PCR amplified from 10 ng of genomic DNA isolated from F. graminearum isolates R-8417, R-8422 and R-8546, F. culmorum isolates R-5106, R-5126 and R-5146, F. moniliforme isolate #4551, F. poae isolates T-0427, T-0534 and T-0756, M. nivale isolates 520, 72 and 18222, and F.
  • ITS1 5' TCCGTAGGTGAACCTGCGG-3'; SEQ ID NO:1
  • ITS4 5'-TCCTCCGCTTATTGATATGC-3'; SEQ ID NO:4
  • PCRs are performed as described in Example 4. PCR products are purified using Promega's Wizard DNA Clean-up kit (Madison, WI).
  • the DNA sequences of the ITS regions are determined by the dideoxy method using the Applied Biosystems (Foster City, CA) automated sequencer with the primers ITS1 (SEQ ID NO:1), ITS2 (5'-GCTGCGTTCTTCATCGATGC-3'; SEQ ID NO:2), ITS4 (SEQ ID NO:4) and the M13 universal -20 (5'-GTAAAACGACGGCCAGT-3'; SEQ ID NO:5) and Reverse (5'-AACAGCTATGACCATG-3'; SEQ ID NO:6) primers.
  • the ITS primers ITS1, ITS2, ITS3, and ITS4 are detailed in White et al. (1990; In: PCR Protocols; Eds.: Innes et al.
  • PCR products from amplifications with F. moniliforme isolate #4551, F. poae isolates T-0427, T-0534 and T-0756 and M. nivale isolates 520, 72 and 18222 are cloned using the Invitrogen Corporation's (San Diego, CA) TA Cloning Kit (part no. K2000-01) using the PCR2.1 cloning vector.
  • DNA is extracted from wheat using a bulk maceration method.
  • the bulk maceration method is used to isolate DNA from several naturally infected wheat heads or stems from the field to optimize the field sampling method for high throughput analysis.
  • Polymerase chain reactions are performed with the GeneAmp® Kit from Perkin-Elmer/Cetus (Norwalk, CT; part no. N808-0009) using 50 mM KCI, 2.5 mM MgCl 2 , 10 mM Tris-HCl, pH8.3, containing 200 ⁇ M of each dTTP, dATP, dCTP, and dGTP, 50 pmol each primer, 2.5 units of Taq polymerase and 10 ng of genomic DNA or 1 ⁇ l of 1:10 diluted plant extract in a final volume of 50 ⁇ l.
  • Reactions are run for 30 - 40 cydes of 15 s at 94°C, 15 s at 50°C - 70°C, and 45 s at 72°C in a Perkin-Elmer/Cetus Model 9600 thermal cycler.
  • the products are analyzed by loading 10 ⁇ l of each PCR sample on a 1.0% agarose gel and electrophoresing.
  • Oligonucleotides are synthesized by, for example, either Integrated DNA Technologies (Coralville, IA) or Midland Certified Reagent Company (Midland, Texas).
  • FIGURE 1 shows an alignment of the sequences of the ITS regions of F . culmorum, F. graminearum, F. poae, M. nivale, and F . moniliforme.
  • Oligonucleotide primers such as those shown below in Table 2 are synthesized according to Example 5 based on analysis of the aligned sequences. Primers are designed to the regions that contain the greatest differences in sequence among the fungal species. Primers are also designed to regions highly conserved among the species in attempt to develop genus-specific primers.
  • ITS1, ITS2, ITS3 and ITS4 are synthesized for testing in combination with the primers specific for the ITS regions.
  • Primers targeted to Fusarium spp. from WO 95/29260 are also used in combination with the newly designed primers to test for novel specificities.
  • nivale JB606 5'GGACTACCTAAACTCTGTT3' (SEQ ID NO: 8) M. nivale JB607 5'AGGGATCATTACCGAGTTT3' (SEQ ID NO: 9) M. nivale JB609 5TCCGGCTTGCAGAAGCGAG3'(SEQ ID NO: 10) M. nivale JB610 5'GAAGGGTGCGGTTTATGGCT3'(SEQ ID NO: 11) M. nivale JB611 5'GCCACCGCCGGTGGAC3'(SEQ ID NO: 12) M. nivale JB612 5'GGTGCTGTCTCTCGGGAC3' (SEQ ID NO: 13) M.
  • nivale JB613 5'AGTCAATCTGAATCAAACTAAG3' (SEQ ID NO: 14) M.
  • nivale JB614 5'CTAAACTCTGTTAATTTTTGTCAA3' (SEQ ID NO: 15) Fusarium spp. 2 JB578 5'CCGCGACGATTACCAG3'(SEQ ID NO: 16) F. gram. + F. culm. 3 JB571 5'TAACGATATGTAAATTACTACGCT3' (SEQ ID NO: 17) F. gram. + F. culm.
  • JB572 5'AAGTTGGGGTTTAACGGC3' (SEQ ID NO: 18) 18S rDNA ITS 1 5TCCGTAGGTGAACCTGCGG3' (SEQ ID NO: 1) 5.8S rDNA ITS2 5'GCTGCGTTCTTCATCGATGC3' (SEQ ID NO: 2) 5.8S rDNA ITS3 5'GCATCGATGAAGAACGCAGC3' (SEQ ID NO: 3) 25S rDNA ITS4 5'TCCTCCGCTTATTGATATGC3' (SEQ ID NO: 4) 1 Fusarium spp. includes F . graminearum. F. culmorum, F. avenaceum, F. poae and F. moniliforme.
  • Fusarium spp. includes F. graminearum, F. culmorum, F. poae, F. moniliforme and F. roseum. 3 Primer combination only tested against F. graminearum, F. culmorum and M. nivale.
  • PCRs are performed according to Example 4 using different primer combinations (Table 3) in an attempt to amplify a single specific fragment.
  • Specific PCR amplification products are produced from primers designed from the ITS regions between the 18S and 25S ribosomal DNA subunits of each fungal strain of interest.
  • Table 3 ITS-Derived Diagnostic PCR Primers Primer Specificity 5' Primer 3'Primer Approximate size of amplified fragment M. nivale JB612 (SEQ ID NO:13) ITS4 (SEQ ID NO:4) 472 bp M. nivale JB613 (SEQ ID NO:14) JB610 (SEQ ID NO:11) 337 bp M.
  • nivale JB614 (SEQ ID NO:15) JB610 (SEQ ID NO:11) 355 bp M.
  • nivale JB613 (SEQ ID NO:14) ITS4 (SEQ ID NO:4) 413 bp M.
  • nivale JB614 (SEQ ID NO:15) ITS4 (SEQ ID NO:4) 431 bp M.
  • nivale JB611 SEQ ID NO:12
  • JB609 SEQ ID NO:10
  • SEQ ID NO:4 450 bp M.
  • nivale ITS1 (SEQ ID NO:1) JB609 (SEQ ID NO:10) 452 bp M. nivale ITS1 (SEQ ID NO:1) JB610 (SEQ ID NO:11) 480 bp M. nivale JB605 (SEQ ID NO:7) JB610 (SEQ ID NO:11) 433 bp M. nivale JB606 (SEQ ID NO:8) JB610 (SEQ ID NO:11) 362 bp M. nivale JB607 (SEQ ID NO:9) JB610 (SEQ ID NO:11) 460 bp Fusarium spp . 1 + M.
  • niv JB605 (SEQ ID NO:7) ITS4 (SEQ ID NO:4) 509 bp. Fusarium spp. 2 JB605 (SEQ ID NO:7) JB578 (SEQ ID NO:16) 417 bp F. gram . + F. culm . 3 JB605 (SEQ ID NO:7) JB572 (SEQ ID NO:18) 440 bp F. gram . + F. culm . 3 JB605 (SEQ ID NO:7) JB571 (SEQ ID NO:17) 400 bp 1 Fusarium spp. includes F. graminearum, F. culmorum, F. avenaceum, F.
  • Total genomic DNA is isolated as described in Example 3 from healthy wheat heads and from wheat heads inoculated with M. nivale, F. graminearum, F. culmorum, or F . avenaceum. PCRs are performed as described in Example 4 testing primer combinations such as those listed in Table 3 against DNA from the wheat tissue. Purified fungal genomic DNAs are obtained as described in Example 1 and PCR assayed as described in Example 4 using the diagnostic primers. Other fungal DNA species and isolates are tested for the ability of the diagnostic primers to cross-react therewith. The results of representative experiments are as follows:
  • M . nivale -specific primer combination JB612 (SEQ ID NO: 13) and ITS4 (SEQ ID NO: 4) amplified a 472 bp fragment from DNA from all of the M. nivale isolates listed in Table 1 and from M. nivale -infected wheat tissue.
  • This primer combination did not amplify a diagnostic fragment from healthy wheat tissue nor from purified genomic DNA from F . graminearum, F. culmorum, F. avenaceum, F. poae or F. moniliforme.
  • This primer combination also did not amplify a diagnostic fragment from purified genomic DNA isolated from the following common cereal pathogens: P. herpotrichoides R- and W-pathotypes, C.
  • Primer combination JB613 (SEQ ID NO:14) and ITS4 (SEQ ID NO:4) amplified a 413 bp fragment
  • primer combination JB614 (SEQ ID NO:15) and ITS4 (SEQ ID NO:4) amplified a 431 bp fragment from DNA from M. nivale isolate #520 and from wheat infected with M. nivale.
  • These primer combinations did not amplify any fragments from healthy wheat tissue, nor from DNA from F. graminearum isolate #R-8422 and F. culmorum isolate #R-5391.
  • M . nivale-specific primer combinations listed in Table 3 amplified a PCR fragment from DNA from M . nivale isolate #520 but not from DNA from F . graminearum isolate #R-8422 nor F . culmorum isolate #R-5391.
  • Primer combination JB605 (SEQ ID NO:7) and ITS4 (SEQ ID NO:4) amplified a 509 bp fragment from DNA from all of the M. nivale isolates listed in Table 1.
  • This primer combination also amplified a 509 bp fragment from DNA from all of the F. graminearum, F. culmorum, F. avenaceum, F. poae and F. moniliforme isolates listed in Table 1.
  • This primer combination did not amplify a diagnostic fragment from purified genomic DNA isolated from the following cereal pathogens: P. herpotrichoides R- and W-pathotypes, C. cereale, D. sorokiniana, C. herbarum, S. glycines, S.
  • Primer combination JB605 SEQ ID NO:7
  • ITS4 SEQ ID NO:4 also amplified a diagnostic fragment from wheat infected with Fusarium spp. but not from healthy wheat.
  • Primer combinations JB605 (SEQ ID NO:7) and JB571 (SEQ ID NO:17), JB605 (SEQ ID NO:7) and JB572 (SEQ ID NO:18), and JB605 (SEQ ID NO:7) and JB578 (SEQ ID NO:16) amplified 400 bp, 440 bp and 417 bp fragments, respectively, from DNA from F . graminearum isolate #R-8422 and F. culmorum isolate #R-5391, but not from M . nivale isolate #520.
  • primer combination JB605 (SEQ ID NO:7) and JB578 (SEQ ID NO:16) amplified a diagnostic fragment from all of the F.
  • herpotrichoides R- and W-pathotypes, C. cereale, D. sorokiniana, C. herbarum, S. glycines, S. tritici, C. arachidicola, S. nodorum, R. solani and S. avenae f.sp. triticea.

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EP98945123A 1997-08-04 1998-07-30 Detection of wheat fungal pathogens using the polymerase chain reaction Expired - Lifetime EP1002134B1 (en)

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US6358680B1 (en) * 1998-02-20 2002-03-19 Syngenta Participations Ag Detection of wheat and barley fungal pathogens using the polymerase chain reaction
US6518020B1 (en) * 1998-09-18 2003-02-11 Heska Corporation Haemobartonella PCR methods and materials
ES2621547T3 (es) 1999-05-28 2017-07-04 Fujirebio Europe N.V. Sondas de ácido nucleico y métodos para detectar patógenos fúngicos clínicamente importantes
US6872523B1 (en) * 2000-05-30 2005-03-29 The Board Of Regents Of The University Of Nebraska Materials and methods for molecular detection of clinically relevant pathogenic fungal species
US6645720B2 (en) * 2001-03-09 2003-11-11 Syngenta Participations Ag Detection of fungal pathogens using the polymerase chain reaction
US6846631B2 (en) * 2001-09-24 2005-01-25 Syngenta Participations Ag Detection of Fusarium species infecting corn using the polymerase chain reaction
US7041456B2 (en) * 2002-04-03 2006-05-09 Syngenta Participations Ag Detection of wheat and barley fungal pathogens which are resistant to certain fungicides using the polymerase chain reaction
CA2484744C (en) * 2002-05-17 2015-09-29 The Government Of The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services, Centers For Disease Control And Prevention Molecular identification of aspergillus species
CA2569190A1 (en) 2004-07-15 2006-01-19 Technische Universitaet Wien Method for the detection of fusarium graminearum
EP2759307B1 (en) 2006-03-29 2016-11-09 Merial Limited Vaccine against Streptococci
CN104630369B (zh) * 2015-02-13 2016-02-24 湖南农业大学 水稻恶苗病菌的pcr检测方法
CN108384834A (zh) * 2018-05-04 2018-08-10 甘肃省农业科学院植物保护研究所 一种青稞茎基腐病燕麦镰孢菌环介导等温扩增检测方法及其应用
CN111471795A (zh) * 2020-05-06 2020-07-31 兰州百源基因技术有限公司 燕麦镰刀菌的rt-qpcr检测的引物、探针、试剂盒及方法
WO2024043830A1 (en) * 2022-08-26 2024-02-29 Denka Life Innovation Research Pte. Ltd. Methods for the detection and identification of fungal species

Family Cites Families (5)

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Publication number Priority date Publication date Assignee Title
US4683195A (en) * 1986-01-30 1987-07-28 Cetus Corporation Process for amplifying, detecting, and/or-cloning nucleic acid sequences
US4683202A (en) * 1985-03-28 1987-07-28 Cetus Corporation Process for amplifying nucleic acid sequences
US5126239A (en) * 1990-03-14 1992-06-30 E. I. Du Pont De Nemours And Company Process for detecting polymorphisms on the basis of nucleotide differences
US5585238A (en) * 1994-04-25 1996-12-17 Ciba-Geigy Corporation Detection of fungal pathogens using the polymerase chain reaction
US5707802A (en) * 1995-01-13 1998-01-13 Ciba Corning Diagnostics Corp. Nucleic acid probes for the detection and identification of fungi

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AU9256298A (en) 1999-03-01
DE69835884D1 (de) 2006-10-26
JP2001512695A (ja) 2001-08-28
US5827695A (en) 1998-10-27
EP1002134A1 (en) 2000-05-24
CA2299299A1 (en) 1999-02-18
CN1265159A (zh) 2000-08-30
CN1264988C (zh) 2006-07-19
WO1999007884A1 (en) 1999-02-18
AU730819B2 (en) 2001-03-15
ATE339516T1 (de) 2006-10-15

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